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2-keto-3-deoxy-D-arabinonate dehydratase complexed with calcium and 2-oxobutyrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.29 α = 90 b = 129.29 β = 90 c = 223.09 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 19.5 97.1 0.123 8.1 3.4 22992 22992
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.3 0.446 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1Q18 2.8 19.48 21834 21834 1156 97.47 0.24084 0.23953 0.26565 0.2504 RANDOM 43.833
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.79 1.79 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.271 r_angle_refined_deg 1.028 r_scangle_it 0.672 r_mcangle_it 0.648 r_scbond_it 0.384 r_mcbond_it 0.361 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.271 r_angle_refined_deg 1.028 r_scangle_it 0.672 r_mcangle_it 0.648 r_scbond_it 0.384 r_mcbond_it 0.361 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.176 r_nbd_refined 0.166 r_symmetry_vdw_refined 0.113 r_metal_ion_refined 0.099 r_chiral_restr 0.085 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2316 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling XFIT data reduction